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| | ==Trypanosoma brucei methionyl-tRNA synthetase in complex with compound Chem 89== | | ==Trypanosoma brucei methionyl-tRNA synthetase in complex with compound Chem 89== |
| - | <StructureSection load='4eg8' size='340' side='right' caption='[[4eg8]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='4eg8' size='340' side='right'caption='[[4eg8]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4eg8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Tryb2 Tryb2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EG8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4eg8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei_TREU927 Trypanosoma brucei brucei TREU927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EG8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0P6:2-AMINOQUINOLIN-8-OL'>0P6</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.596Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAS:S-(DIMETHYLARSENIC)CYSTEINE'>CAS</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0P6:2-AMINOQUINOLIN-8-OL'>0P6</scene>, <scene name='pdbligand=CAS:S-(DIMETHYLARSENIC)CYSTEINE'>CAS</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4eg1|4eg1]], [[4eg3|4eg3]], [[4eg4|4eg4]], [[4eg5|4eg5]], [[4eg6|4eg6]], [[4eg7|4eg7]], [[4ega|4ega]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4eg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eg8 OCA], [https://pdbe.org/4eg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eg8 RCSB], [https://www.ebi.ac.uk/pdbsum/4eg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eg8 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tb10.70.6470 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=999953 TRYB2])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine--tRNA_ligase Methionine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.10 6.1.1.10] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4eg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eg8 OCA], [http://pdbe.org/4eg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4eg8 RCSB], [http://www.ebi.ac.uk/pdbsum/4eg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4eg8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q38C91_TRYB2 Q38C91_TRYB2] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Methionine--tRNA ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Tryb2]] | + | [[Category: Trypanosoma brucei brucei TREU927]] |
| - | [[Category: Fan, E]] | + | [[Category: Fan E]] |
| - | [[Category: Hol, W G.J]] | + | [[Category: Hol WGJ]] |
| - | [[Category: Kim, J E]] | + | [[Category: Kim JE]] |
| - | [[Category: Koh, C Y]] | + | [[Category: Koh CY]] |
| - | [[Category: Shibata, S]] | + | [[Category: Shibata S]] |
| - | [[Category: Verlinde, C L.M J]] | + | [[Category: Verlinde CLMJ]] |
| - | [[Category: Aar]]
| + | |
| - | [[Category: Aminoacyl-trna synthetase]]
| + | |
| - | [[Category: Atp binding]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Ligase-ligase inhibitor complex]]
| + | |
| - | [[Category: Metr]]
| + | |
| - | [[Category: Nucleotide binding]]
| + | |
| - | [[Category: Parasite]]
| + | |
| - | [[Category: Protein-inhibitor complex]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Rossmann-fold]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: Trna binding]]
| + | |
| Structural highlights
4eg8 is a 2 chain structure with sequence from Trypanosoma brucei brucei TREU927. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.596Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q38C91_TRYB2
Publication Abstract from PubMed
To guide development of new drugs targeting methionyl-tRNA synthetase (MetRS) for treatment of human African trypanosomiasis, crystal structure determinations of Trypanosoma brucei MetRS in complex with its substrate methionine and its intermediate product methionyl-adenylate were followed by those of the enzyme in complex with high-affinity aminoquinolone inhibitors via soaking experiments. Drastic changes in conformation of one of the two enzymes in the asymmetric unit allowed these inhibitors to occupy an enlarged methionine pocket and a new so-called auxiliary pocket. Interestingly, a small low-affinity compound caused the same conformational changes, removed the methionine without occupying the methionine pocket, and occupied the previously not existing auxiliary pocket. Analysis of these structures indicates that the binding of the inhibitors is the result of conformational selection, not induced fit.
Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection.,Koh CY, Kim JE, Shibata S, Ranade RM, Yu M, Liu J, Gillespie JR, Buckner FS, Verlinde CL, Fan E, Hol WG Structure. 2012 Aug 14. PMID:22902861[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Koh CY, Kim JE, Shibata S, Ranade RM, Yu M, Liu J, Gillespie JR, Buckner FS, Verlinde CL, Fan E, Hol WG. Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection. Structure. 2012 Aug 14. PMID:22902861 doi:http://dx.doi.org/10.1016/j.str.2012.07.011
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